ppEffect Report

Overview of the dataset

Attribute Content
Object name ara_root_simple
Cell number 4709
Gene number 3909
Active assay SCT
Reductions pca, umap, tsne
Up-regulated pp.Score (Q2) 0.091792
Up-regulated Groups in terms of Q2 0 , 1 , 3 , 4 , 10 , 11
Up-regulated pp.Score (Q3) 0.2274613
Up-regulated Groups in terms of Q3 1 , 3 , 4
Down-regulated pp.Score (Q2)
-0.072741
Down-regulated Groups in terms of Q2
1 , 3 , 4 , 7 , 10 , 11 , 15
Down-regulated pp.Score (Q1)
-0.012831
Down-regulated Groups in terms of Q1
7 , 10 , 15

Gene number: representing the gene numbers in the activate assay.

Reductions: representing the dimension reduction methods conducted in this dataset.

Up-regulated pp.Score (Q2) : representing the median expression value of enzymolysis induced genes (Up_ppDEGs).

Up-regulated Groups in terms of Q2 : calculating the median of pp.Score in each cell group, then to figure out which clusters have higher pp.Scores than the pp.Score (Q2).

Up-regulated pp.Score (Q3) : representing The third quartile(Q3), also known as the higher quartile, is equal to the 75% of all the values in the sample arranged from the smallest to the largest of enzymolysis induced genes (Up_ppDEGs).

Up-regulated Groups in terms of Q3 : calculating the median of pp.Score in each cell group, then to figure out which clusters have higher pp.Scores than the pp.Score (Q3).

Down-regulated pp.Score (Q2) : representing the median expression value of enzymolysis induced genes (Down_ppDEGs).

Down-regulated Groups in terms of Q2 : calculating the median of pp.Score in each cell group, then to figure out which clusters have lower pp.Scores than the pp.Score (Q2).

Down-regulated pp.Score (Q1) : representing The first quartile(Q1), also known as the lower quartile, is equal to the smallest 25% of all the pp.Score values of enzymolysis induced genes (Down_ppDEGs).

Down-regulated Groups in terms of Q1 : calculating the median of pp.Score in each cell group, then to figure out which clusters have lower pp.Scores than the pp.Score (Q1).

Overlap between ppDEGs and HVGs

In this dataset, we totally have 3000 highly variable genes (HVGs), and all the HVGs will be used for PCA analysis following up.

The number of Up_ppDEGs is 917. The intersection between HVGs and Up_ppDEGs were 344 (genes), which means that 37.51% Up_ppDEGs belong to HVGs.

The number of Down_ppDEGs is 2518.The intersection between HVGs and Down_ppDEGs were 688 (genes), which means that 27.32% Down_ppDEGs belong to HVGs.

The extent of ppEffects in each cell

In this panel, your can see the distribution of ppEffects in each cells by UMAP plot. The darker the cell color, the more severely it is affected by enzymatic hydrolysis

Groups affected by ppEffect

In this panel, we use the violin plot to display which groups were highly affected by ppEffect.

Up-regulated groups

The red dotted line presented the median expression value of enzymolysis induced genes (Up_ppDEGs). The median expression value of Up_ppDEGs (Up-regulated pp.Score Q2) in this dataset is 0.091792 .

The yellow dotted line presented the higher quartile expression value of enzymolysis induced genes (Up_ppDEGs). The higher quartile expression value of Up_ppDEGs (Up-regulated pp.Score Q3) in this dataset is 0.2274613 .

In this panel, we use the Dotplot to display which groups were highly affected by Up_ppDEGs.

Down-regulated groups

The red dotted line presented the median expression value of enzymolysis induced genes (Down_ppDEGs). The median expression value of Down_ppDEGs (Down-regulated pp.Score Q2) in this dataset is -0.072741 .

The yellow dotted line presented the higher quartile expression value of enzymolysis induced genes (Down_ppDEGs). The lower quartile expression value of Down_ppDEGs (Down-regulated pp.Score Q1) in this dataset is -0.1059478 .

In this panel, we use the Dotplot to display which groups were highly affected by Down_ppDEGs.

Overlap between ppDEGs and cluster markers

This panel display the intersection between Up_ppDEGs and marker genes cluster by cluster.

This panel display the intersection between Down_ppDEGs and marker genes cluster by cluster.